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Updated: Apr 28, 2026
A High Throughput, Multiplexed and Targeted Proteomic CSF Assay to Quantify Neurodegenerative Biomarkers and Apolipoprotein E Isoforms Status
Published on: October 20, 2016
Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation
Andrew J Percy1, Juncong Yang1, Andrew G Chambers1
1University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria , Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z 7X8, Canada.
We developed a rapid, antibody-free method for quantifying 130 protein biomarkers in cerebrospinal fluid (CSF) using multiplexed selected reaction monitoring (SRM). This approach enables efficient biomarker discovery and validation for central nervous system (CNS) diseases.
Area of Science:
- Proteomics
- Biomarker Discovery
- Mass Spectrometry
Background:
- Multiplexed quantitation is crucial for biomarker discovery, validation, and therapeutic monitoring.
- Selected/Multiple Reaction Monitoring (SRM/MRM) with isotopically labeled standards is a key technology for quantifying protein biomarkers.
- Cerebrospinal fluid (CSF) is vital for studying central nervous system (CNS) diseases.
Purpose of the Study:
- To develop a rapid, antibody- and fractionation-free SRM/MRM approach for highly multiplexed protein biomarker quantitation in human CSF.
- To establish a method for quantifying a broad panel of candidate protein biomarkers in CSF.
Main Methods:
- Optimization of peptide transitions and denaturation/digestion protocols.
- Screening for transition interferences.
- Protein quantitation using peptide standard curves in a bottom-up proteomic workflow.
- Utilized a complex mixture of peptide standards for quantification.
Main Results:
- Developed a reproducible method with average coefficients of variation <1% for retention time and <6% for signal.
- Quantified 130 proteins from 311 interference-free peptides in a single 43-minute run.
- Covered a wide range of protein concentrations, from serum albumin (118 μg/mL) to apolipoprotein C-I (550 pg/mL).
Conclusions:
- The developed method represents the most highly multiplexed and broadest panel of candidate protein biomarkers in human CSF reported to date.
- This approach is suitable for subsequent verification studies on patient samples.
- The antibody- and fractionation-free strategy enhances efficiency in biomarker analysis.
